Semantic WikiPathwaysAndra Waagmeester

Department of Bioinformatics - BiGCaT 2

Overview

• Introduction to WikiPathways• GPML• Pathway to RDF conversion• Vocabularies used• Obtaining identifiers URIs pathways and

pathway elements• Example queries• Identifier mapping

Department of Bioinformatics - BiGCaT 3

WikiPathways

• Curated by the community• Built on top of Mediawiki framework• Live demo

Department of Bioinformatics - BiGCaT 4

GPML - GenMAPP Pathway Markup Language• XML-based format.• XML representation of GenMAPP MAPP

format• Recognised by WikiPathways, Pathvisio

and Cytoscape

Department of Bioinformatics - BiGCaT 5

Department of Bioinformatics - BiGCaT 6

Pathway to RDF conversion

Department of Bioinformatics - BiGCaT 7

WP to RDF conversion

Department of Bioinformatics - BiGCaT 8

Vocabularies used

• Internal (vocabularies.wikipathways.org)– GPML– WP

• External– Biopax3– Bibo– Foaf– tbd

Department of Bioinformatics - BiGCaT 9

Identifiers.org

• Providing resolvable persistent URIs.• Based on Miriam

(http://www.ebi.ac.uk/miriam)• Textual Pathway identifiers (xrefs)

converted to identifiers.org uri through the miriam api

Department of Bioinformatics - BiGCaT 10

Example query (1)

List pathways and their speciesSELECT DISTINCT ?organism ?labelWHERE { ?concept wp:organism ?organism . ?organism rdfs:label ?label . }

http://sparqlbin.com/#4f91f23a032a87cc46c5a526a6da673a

Department of Bioinformatics - BiGCaT 11

Example query (2)

List all datasource currently captured in WikiPathways and count

the number of entries per data source:

SELECT DISTINCT ?datasource count(?datasource) as ?numberEntries

WHERE {

?concept dc:source ?datasource .

}

ORDER BY DESC(?numberEntries)

http://sparqlbin.com/#a86569fa8a5ae4b004fdf2432b3ce98c

Department of Bioinformatics - BiGCaT 12

Example query (3)

Extract the amount of pathways edited per contributorSELECT DISTINCT ?contributor COUNT(?pathway) as ?pathwaysEdited

WHERE {

 ?pathway dc:contributor ?contributor

}

ORDER BY DESC(?pathwaysEdited)

Department of Bioinformatics - BiGCaT 13

Example query nExtracting Inchi out of ChEMBLSELECT ?concept ?inchi ?pathway ?identifier

WHERE {

?concept dcterms:isPartOf ?pathway .

?concept dc:source "ChEMBL compound"^^xsd:string .

?concept dc:identifier ?identifier .

SERVICE <http://rdf.farmbio.uu.se/chembl/sparql>{

?s rdfs:label ?chidentifier .

?s <http://www.blueobelisk.org/chemistryblogs/inchi> ?inchi .}

FILTER (xsd:string(?chidentifier)= xsd:string(?identifier)) .

}

Department of Bioinformatics - BiGCaT 14

Federated query

• Required unified URIs• Identifier mapping

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Identifier mapping

• Data enrichment• Query expansion• Unified identifier conversion

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Data enrichment

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Unified Identifiers

Department of Bioinformatics - BiGCaT 18

Query expansion

Department of Bioinformatics - BiGCaT 19

Acknowledgements

• the Innovative Medicines Initiative Joint (n°115191,

FP7/2007-2013)

• The NIH National Institute for General Medical Sciences

(R01-GM100039)

Department of Bioinformatics - BiGCaT 20

Acknowledgement

Gladstone Institute

•Alex Pico

Maastricht University

•Martina Kutmon

•Egon Willighagen

•Chris Evelo

Manchester University

•Alasdair Gray

•Christian BreninkMeijer

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Resources:

• WikiPathways: www.wikipathways.org

• Pathvisio: www.pathvisio.org

• RDF: rdf.wikipathways.org

• SPARQL: sparql.wikipathways.org

• Vocabularies:vocabularies.wikipathways.org

• BridgeDb: www.bridgeDb.org

• IMS: ondex2.cs.man.ac.uk:9090/QueryExpander/)